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- PDB-5me1: Structure of the 30S Pre-Initiation Complex 2 (30S IC-2) Stalled ... -

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Basic information

Entry
Database: PDB / ID: 5me1
TitleStructure of the 30S Pre-Initiation Complex 2 (30S IC-2) Stalled by GE81112
Components
  • (30S ribosomal protein ...) x 20
  • (Translation initiation factor IF- ...) x 4
  • 16S ribosomal RNA
  • fMet-tRNA
KeywordsRIBOSOME / Initiation of Translation
Function / homology
Function and homology information


ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / ribosomal small subunit binding / Group I intron splicing / RNA folding / chaperone-mediated protein folding / negative regulation of translational initiation ...ribosome disassembly / guanosine tetraphosphate binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / ribosomal small subunit binding / Group I intron splicing / RNA folding / chaperone-mediated protein folding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / response to cold / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / translational initiation / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Elongation factor Tu domain 2 / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S21 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily
Similarity search - Domain/homology
N-FORMYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S16 / Translation initiation factor IF-3 / Small ribosomal subunit protein bS16 ...N-FORMYLMETHIONINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S16 / Translation initiation factor IF-3 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Translation initiation factor IF-3 / Translation initiation factor IF-2 / Translation initiation factor IF-3 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Thermus thermophilus (bacteria)
Geobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsLopez-Alonso, J.P. / Fabbretti, A. / Kaminishi, T. / Iturrioz, I. / Brandi, L. / Gil Carton, D. / Gualerzi, C. / Fucini, P. / Connell, S.
CitationJournal: Nucleic Acids Res / Year: 2017
Title: Structure of a 30S pre-initiation complex stalled by GE81112 reveals structural parallels in bacterial and eukaryotic protein synthesis initiation pathways.
Authors: Jorge P López-Alonso / Attilio Fabbretti / Tatsuya Kaminishi / Idoia Iturrioz / Letizia Brandi / David Gil-Carton / Claudio O Gualerzi / Paola Fucini / Sean R Connell /
Abstract: In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the ...In bacteria, the start site and the reading frame of the messenger RNA are selected by the small ribosomal subunit (30S) when the start codon, typically an AUG, is decoded in the P-site by the initiator tRNA in a process guided and controlled by three initiation factors. This process can be efficiently inhibited by GE81112, a natural tetrapeptide antibiotic that is highly specific toward bacteria. Here GE81112 was used to stabilize the 30S pre-initiation complex and obtain its structure by cryo-electron microscopy. The results obtained reveal the occurrence of changes in both the ribosome conformation and initiator tRNA position that may play a critical role in controlling translational fidelity. Furthermore, the structure highlights similarities with the early steps of initiation in eukaryotes suggesting that shared structural features guide initiation in all kingdoms of life.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Advisory / Data collection / Derived calculations
Category: em_imaging_optics / em_software ...em_imaging_optics / em_software / pdbx_validate_polymer_linkage / struct_conn
Item: _em_imaging_optics.energyfilter_name / _em_software.name
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.6Nov 13, 2019Group: Data collection / Other / Category: symmetry
Item: _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M
Revision 1.7Apr 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Assembly

Deposited unit
A: 16S ribosomal RNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein S21
V: Translation initiation factor IF-1
W: Translation initiation factor IF-2
Y: Translation initiation factor IF-3
Z: Translation initiation factor IF-3
X: fMet-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)953,58827
Polymers953,41026
Non-polymers1771
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules AX

#1: RNA chain 16S ribosomal RNA


Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 802133627
#26: RNA chain fMet-tRNA


Mass: 24818.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 3JCN / Source: (natural) Escherichia coli K-12 (bacteria) / References: GenBank: 731469900

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30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU

#2: Protein 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V0
#3: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V3
#4: Protein 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7V8
#5: Protein 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W1
#6: Protein 30S ribosomal protein S6


Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02358
#7: Protein 30S ribosomal protein S7


Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P02359
#8: Protein 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7W7
#9: Protein 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7X3
#10: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R5
#11: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7R9
#12: Protein 30S ribosomal protein S12


Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7S3
#13: Protein 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Taken from PDB entry 4YBB / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpsM, b3298, JW3260 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S9
#14: Protein 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG59
#15: Protein 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0ADZ4
#16: Protein 30S ribosomal protein S16


Mass: 11464.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: D8AGC4, UniProt: A0A0U4BH30*PLUS
#17: Protein 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0AG63
#18: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7T7
#19: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U3
#20: Protein 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P0A7U7
#21: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Taken from PDB entry 4YBB / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P68679

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Translation initiation factor IF- ... , 4 types, 4 molecules VWYZ

#22: Protein Translation initiation factor IF-1


Mass: 8247.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Taken from PDB entry 1HR0
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: infA, TTHA1669 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHR1
#23: Protein Translation initiation factor IF-2


Mass: 97498.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Taken from PDB entry 3JCN / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: infB, gicD, ssyG, b3168, JW3137 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A705
#24: Protein Translation initiation factor IF-3


Mass: 19717.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Taken from PDB entry 1TIF
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: infC / Production host: Escherichia coli (E. coli) / References: UniProt: P03000
#25: Protein Translation initiation factor IF-3


Mass: 16667.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Taken from PDB entry 2IFE / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A192C6K3, UniProt: P0A707*PLUS

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Non-polymers , 1 types, 1 molecules

#27: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO3S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 30S Pre-Initiation Complex IC-2 Stalled by GE81112 / Type: RIBOSOME / Entity ID: #1-#26 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisTrisHCl1
27 mMMagnesium chlorideMgCl21
360 mMAmmonium acetateCH3CO2NH41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 74183 X / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 17 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 261
EM imaging opticsEnergyfilter name: In-column Omega Filter
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1RELION1.4particle selection
2DigitalMicrographimage acquisition
4CTFFIND4CTF correction
7Situsmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Coot0.8.3model refinementFor minimizing the conformation of the linking residues of ligands that were fitted as multiple independent bodies i.e. domains G2-C1 and C2 of IF2, and residues 1-72 and 73-76 of the mRNA.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 174142
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26776 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Details: The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the ...Details: The fitting of the model to the EM volume was performed through rigid body fitting. The head and the body of the 30S were treated as independent bodies. Due to the low resolution of the volume, the conformation of the linking bases was not minimized. In addition, some of the clashes of the model are produced by flexible loops or protein side chains that were not refined.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
14YBB

4ybb

4YBB1
23JCN

3jcn

b3JCN2
33JCN

3jcn

v3JCN2
41HR0

1hr0

W1HR03
52IFE

2ife

A2IFE490-180
61TIF

1tif

A1TIF53-78

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